Evaluate gene sets by cell type-specific gene expression

Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(stringr)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name

## [1] "Astro"

graph_weight

## [1] "2.0"

Check the expression of each gene set in each brain-related cell type

Read in gene info and gene set assignments

file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

length(assayed_genes)

## [1] 2000

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    41.0    42.0    43.0    43.4    45.0    45.0

length(n_genes)

## [1] 40

sort(n_genes)

##  [1] 41 41 41 42 42 42 42 42 42 42 42 43 43 43 43 43 43 43 43 43 43 43 44 44 44
## [26] 44 44 44 45 45 45 45 45 45 45 45 45 45 45 45

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}

## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"

table(is.na(a2s))

## 
## FALSE  TRUE 
##  1643   357

table(a2s == assayed_genes, useNA = 'ifany')

## 
## FALSE  TRUE  <NA> 
##    21  1622   357

gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]

##      sym_in_data   sym_limma
##  1:       BTBD11       ABTB3
##  2:    LINC01006    RNF32-DT
##  3:    LINC01185      REL-DT
##  4:   ZRANB2-AS2   ZRANB2-DT
##  5:    LINC00271     AHI1-DT
##  6:     RFX3-AS1     RFX3-DT
##  7:    COX10-AS1    COX10-DT
##  8:   SUCLG2-AS1   SUCLG2-DT
##  9:      C5orf17   LINC02899
## 10:     OSMR-AS1     OSMR-DT
## 11:  C8orf37-AS1 CFAP418-AS1
## 12: CTB-178M22.2   TENM2-AS1
## 13:    LINC00637 PPP1R13B-DT
## 14:         MPP6    MPHOSPH6
## 15:      C7orf61      SPACDR
## 16:      C3orf35       APRG1
## 17:       HRAT92    PDGFA-DT
## 18:    LINC00884  ATP13A3-DT
## 19:    LINC01137  ZC3H12A-DT
## 20: TMEM161B-AS1 TMEM161B-DT
## 21:      MAFG-DT       MILIP
##      sym_in_data   sym_limma

gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)

## [1] 2000    3

gene_info[1:5,]

##    sym_in_data sym_limma gene_symbol
## 1:        CD38      CD38        CD38
## 2:     PRKAR2B   PRKAR2B     PRKAR2B
## 3:        ASB4      ASB4        ASB4
## 4:       USH1C     USH1C       USH1C
## 5:    ARHGAP44  ARHGAP44    ARHGAP44

t1 = table(gene_info$gene_symbol)
table(t1)

## t1
##    1 
## 2000

Read in cell type-specific expression data

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

ct = fread("../Annotation/rna_single_cell_type.tsv.gz")
dim(ct)

## [1] 1587110       4

ct[1:5,]

##               Gene Gene name             Cell type  nTPM
## 1: ENSG00000000003    TSPAN6            Adipocytes 149.5
## 2: ENSG00000000003    TSPAN6 Alveolar cells type 1   6.1
## 3: ENSG00000000003    TSPAN6 Alveolar cells type 2  10.5
## 4: ENSG00000000003    TSPAN6            Astrocytes  13.9
## 5: ENSG00000000003    TSPAN6               B-cells   1.5

length(unique(ct$`Cell type`))

## [1] 79

table(ct$`Cell type`)

## 
##                      Adipocytes           Alveolar cells type 1 
##                           20090                           20090 
##           Alveolar cells type 2                      Astrocytes 
##                           20090                           20090 
##                         B-cells             Basal keratinocytes 
##                           20090                           20090 
##           Basal prostatic cells         Basal respiratory cells 
##                           20090                           20090 
## Basal squamous epithelial cells                   Bipolar cells 
##                           20090                           20090 
##          Breast glandular cells      Breast myoepithelial cells 
##                           20090                           20090 
##                  Cardiomyocytes                  Cholangiocytes 
##                           20090                           20090 
##                      Club cells           Collecting duct cells 
##                           20090                           20090 
##        Cone photoreceptor cells                Cytotrophoblasts 
##                           20090                           20090 
##                 dendritic cells              Distal enterocytes 
##                           20090                           20090 
##            Distal tubular cells                    Ductal cells 
##                           20090                           20090 
##                Early spermatids      Endometrial ciliated cells 
##                           20090                           20090 
##       Endometrial stromal cells               Endothelial cells 
##                           20090                           20090 
##           Enteroendocrine cells                 Erythroid cells 
##                           20090                           20090 
##              Excitatory neurons        Exocrine glandular cells 
##                           20090                           20090 
##       Extravillous trophoblasts                     Fibroblasts 
##                           20090                           20090 
##   Gastric mucus-secreting cells     Glandular and luminal cells 
##                           20090                           20090 
##                    granulocytes                 Granulosa cells 
##                           20090                           20090 
##                     Hepatocytes                  Hofbauer cells 
##                           20090                           20090 
##                Horizontal cells              Inhibitory neurons 
##                           20090                           20090 
##         Intestinal goblet cells                       Ionocytes 
##                           20090                           20090 
##                   Kupffer cells                Langerhans cells 
##                           20090                           20090 
##                 Late spermatids                    Leydig cells 
##                           20090                           20090 
##                     Macrophages                     Melanocytes 
##                           20090                           20090 
##                Microglial cells                       monocytes 
##                           20090                           20090 
##           Mucus glandular cells               Muller glia cells 
##                           20090                           20090 
##                        NK-cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes      Pancreatic endocrine cells 
##                           20090                           20090 
##                    Paneth cells               Peritubular cells 
##                           20090                           20090 
##                    Plasma cells       Prostatic glandular cells 
##                           20090                           20090 
##            Proximal enterocytes          Proximal tubular cells 
##                           20090                           20090 
##      Respiratory ciliated cells         Rod photoreceptor cells 
##                           20090                           20090 
##             Salivary duct cells                   Schwann cells 
##                           20090                           20090 
##          Serous glandular cells                   Sertoli cells 
##                           20090                           20090 
##               Skeletal myocytes             Smooth muscle cells 
##                           20090                           20090 
##                   Spermatocytes                   Spermatogonia 
##                           20090                           20090 
##       Squamous epithelial cells        Suprabasal keratinocytes 
##                           20090                           20090 
##            Syncytiotrophoblasts                         T-cells 
##                           20090                           20090 
##                     Theca cells         Thymic epithelial cells 
##                           20090                           20090 
##          Undifferentiated cells 
##                           20090

cell_group = fread("../Annotation/rna_single_cell_type_brain.tsv")
dim(cell_group)

## [1] 16  2

cell_group[1:2,]

##             Cell_type Cell_group
## 1: Excitatory neurons   Neuronal
## 2: Inhibitory neurons   Neuronal

ct = ct[`Cell type` %in% cell_group$Cell_type,]
table(ct$`Cell type`)

## 
##                      Astrocytes                         B-cells 
##                           20090                           20090 
##                   Bipolar cells        Cone photoreceptor cells 
##                           20090                           20090 
##              Excitatory neurons                Horizontal cells 
##                           20090                           20090 
##              Inhibitory neurons                Microglial cells 
##                           20090                           20090 
##               Muller glia cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes                    Plasma cells 
##                           20090                           20090 
##         Rod photoreceptor cells                   Schwann cells 
##                           20090                           20090 
##                         T-cells 
##                           20090

Check gene expression for each gene set

dim(gene_info)

## [1] 2000    3

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]

  n_genes = sum(genes %in% ct$`Gene name`)
  print(sprintf("found %d genes.", n_genes))

  if(n_genes == 0) { next }

  df = ct[`Gene name` %in% genes,]
  dim(df)
  df[1:2,]
  
  stopifnot(all(str_to_lower(df$`Cell type`) %in% 
                  str_to_lower(cell_group$Cell_type)))
  
  mat1 = match(str_to_lower(df$`Cell type`), 
               str_to_lower(cell_group$Cell_type))
  
  df = cbind(df, cell_group[mat1,])
  df[1:2,]
  
  df$Cell_type = factor(df$Cell_type, levels = cell_group$Cell_type)
  df$Cell_group = factor(df$Cell_group, 
                         levels = unique(cell_group$Cell_group))
  
  p1 = ggplot(df, aes(x=Cell_type, y=log10(nTPM + 0.1), fill=Cell_group)) + 
    geom_boxplot() + xlab("Cell type") + ggtitle(set_k) + 
    theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
    scale_fill_brewer(palette="RdBu")

  print(p1)
}

## [1] 1
##  [1] "GPNMB"         "RNF165"        "ARHGAP27"      "CCDC141"      
##  [5] "AGBL2"         "ZCCHC18"       "RAB39A"        "SP140L"       
##  [9] "WNT7B"         "RP1-15D23.2"   "CCDC192"       "BAALC-AS2"    
## [13] "LINC02196"     "LINC02745"     "KCNG1"         "RASGRP2"      
## [17] "ARHGAP15"      "ANGPT2"        "PCDH11Y"       "CACNA1I"      
## [21] "TNNT2"         "HS3ST2"        "SLC6A6"        "SRRM4"        
## [25] "KCNH5"         "RIT2"          "KCNJ16"        "CATIP"        
## [29] "SPATA2L"       "VWA5B1"        "SAMD3"         "PPP1R36"      
## [33] "VAT1L"         "NXNL1"         "VSTM2B"        "POTEG"        
## [37] "STARD10"       "LINC02869"     "RP11-958J22.1" "MTRNR2L1"     
## [41] "AF038458.3"    "RP5-1015P16.1" "CTD-2201E18.6"
## [1] "found 34 genes."

## [1] 2
##  [1] "RPH3A"         "PDE10A"        "PEX5L"         "ST6GALNAC5"   
##  [5] "KIRREL3"       "MMP16"         "NDST3"         "OTOGL"        
##  [9] "FSTL5"         "MTSS1"         "HOPX"          "ERICH3"       
## [13] "CCBE1"         "TAFA1"         "GRM7"          "AP000233.4"   
## [17] "MRPS9-AS2"     "LINC01266"     "RP11-170M17.1" "CCDC26"       
## [21] "AC011288.2"    "MIR181A1HG"    "LINC01036"     "AC079807.4"   
## [25] "LINC00326"     "KIF5C-AS1"     "RP1-232L24.3"  "LINC01934"    
## [29] "CXXC4-AS1"     "RP11-410D17.2" "RP11-436F23.1" "RP11-380P13.1"
## [33] "LINC00923"     "RP11-586K2.1"  "AB015752.3"    "RP4-809F18.1" 
## [37] "LINC02389"     "MTRNR2L8"      "CTXND1"        "RP11-413N10.3"
## [41] "RP11-57G22.3"  "RP11-640F22.1" "RP11-320L2.1"  "RP11-120J1.2" 
## [45] "KRTAP5-AS1"   
## [1] "found 17 genes."

## [1] 3
##  [1] "SIDT1"         "ANKRD7"        "LRRC9"         "RGS22"        
##  [5] "PEBP4"         "KCTD1"         "PLXNC1"        "LIX1"         
##  [9] "SAXO1"         "KIF6"          "FREM1"         "VWA3B"        
## [13] "NRG4"          "DNAH12"        "VWA3A"         "LINC01006"    
## [17] "ENO4"          "HMGN5"         "CRPPA"         "AC105760.2"   
## [21] "LINC01185"     "LINC01239"     "LINC01695"     "RP11-132E11.2"
## [25] "LINC01358"     "RP11-624M8.1"  "NECTIN3-AS1"   "RP11-114J13.1"
## [29] "LINC01340"     "LINC02615"     "CTB-178M22.2"  "RP11-708B6.2" 
## [33] "RP11-867G2.8"  "RP11-266O8.1"  "LINC02326"     "RP11-352M15.1"
## [37] "CRTC3-AS1"     "RP11-290O12.2" "RP5-847G17.1"  "RP11-335E8.3" 
## [41] "RP1-84D21.2"   "RP11-341N18.1" "RP11-788A4.3"  "DISP3"        
## [45] "RP11-348F1.3" 
## [1] "found 19 genes."

## [1] 4
##  [1] "LRRC7"         "PSD"           "SEL1L2"        "KIAA1549L"    
##  [5] "WARS1"         "SPOCK1"        "PRELID2"       "GAS7"         
##  [9] "SYT7"          "KLF6"          "TESC"          "KLHL4"        
## [13] "USP9Y"         "MOB3B"         "TSHZ3"         "QRICH2"       
## [17] "DPP6"          "COL5A1"        "AK7"           "ADAM12"       
## [21] "CNKSR2"        "SEC24D"        "COX7A1"        "LRRC2"        
## [25] "NLGN4Y"        "PGM2L1"        "DEPP1"         "SLC38A11"     
## [29] "TPST1"         "TTTY14"        "CSMD1"         "CCK"          
## [33] "DPYD"          "MEG3"          "RP11-513I15.6" "MIR34AHG"     
## [37] "SATB1-AS1"     "TTTY10"        "LINC00278"     "IQCM"         
## [41] "LINC01322"     "PTCHD4"        "MIR23AHG"     
## [1] "found 34 genes."

## [1] 5
##  [1] "TMEM241"       "RERG"          "C2CD6"         "ADRA1B"       
##  [5] "PAH"           "GPR39"         "NAP1L3"        "GRM3"         
##  [9] "DIO2"          "LCNL1"         "RP1-292B18.4"  "PLCG1-AS1"    
## [13] "EPS15-AS1"     "AP000282.2"    "LINC01344"     "RP1-45C12.1"  
## [17] "AC007682.1"    "RP11-142A5.1"  "RBMS3-AS3"     "AC079305.11"  
## [21] "RP11-154H17.1" "MEF2C-AS2"     "HS3ST5"        "F11-AS1"      
## [25] "LINC01301"     "RP1-84O15.2"   "LINC00534"     "RP11-317N12.1"
## [29] "ZFHX4-AS1"     "RP11-431M3.1"  "RP11-260G13.1" "RP11-526N18.1"
## [33] "RP11-242P2.1"  "RP11-524F11.2" "RP11-103J8.1"  "RP11-561I11.4"
## [37] "LINC00540"     "LINC01727"     "CH17-174L20.1" "RP3-383B8.1"  
## [41] "RP11-624A4.2"  "RP11-399K19.1" "MEIKIN"        "MAFG-DT"      
## [1] "found 12 genes."

## [1] 6
##  [1] "DNASE1L1" "FAR2"     "PPEF1"    "EPB41L4B" "IQCH"     "CEMIP"   
##  [7] "FRK"      "HSD11B1"  "EPSTI1"   "GULP1"    "CCDC102B" "AXDND1"  
## [13] "TMEM130"  "EPHX4"    "SSR4"     "KCNIP1"   "THSD4"    "ARHGAP8" 
## [19] "SYN1"     "DCN"      "ABCA7"    "ATP2B3"   "CASS4"    "CELF4"   
## [25] "SUSD1"    "CHD5"     "SPP1"     "DUSP1"    "AIF1L"    "LOXL1"   
## [31] "MICAL1"   "DOCK10"   "SLC44A5"  "SH3GL1"   "COL6A2"   "FBXO32"  
## [37] "ITGA2"    "ENOX2"    "MAP1A"    "NPTX1"    "LRRC8C"   "CTXN1"   
## [43] "MB21D2"  
## [1] "found 43 genes."

## [1] 7
##  [1] "MAP2K6"       "ID1"          "C4orf45"      "RP11-793A3.2" "HGF"         
##  [6] "RASSF1"       "FOSL2"        "PPP1R15A"     "GADD45B"      "RELB"        
## [11] "IL1R1"        "IGSF21"       "ID3"          "TBX2"         "ITIH5"       
## [16] "HELB"         "KLF2"         "GALNT8"       "JUND"         "ZSWIM4"      
## [21] "IRAK2"        "ITPRIP"       "SLC43A1"      "RASSF3"       "RHPN1"       
## [26] "ATF3"         "NFIL3"        "FOS"          "JUNB"         "PLEKHG5"     
## [31] "RND1"         "HAP1"         "CAVIN1"       "CHST6"        "MAFF"        
## [36] "MITF"         "SAMD11"       "SLC6A9"       "CFI"          "S1PR3"       
## [41] "RP1-187B23.1" "RP3-365E2.1" 
## [1] "found 39 genes."

## [1] 8
##  [1] "ATP11A"                  "RASD1"                  
##  [3] "CLIC5"                   "ELL2"                   
##  [5] "ACAT2"                   "CRISPLD1"               
##  [7] "SLC44A3"                 "SVEP1"                  
##  [9] "PCED1B"                  "PAPPA"                  
## [11] "GPC6"                    "PROS1"                  
## [13] "F5"                      "OSMR-AS1"               
## [15] "RP11-255O19.2"           "VCAN"                   
## [17] "ST6GAL1"                 "FRY"                    
## [19] "PIR"                     "P3H2"                   
## [21] "RASL12"                  "SPAG1"                  
## [23] "AEBP1"                   "CCL2"                   
## [25] "PRRX1"                   "MAN1C1"                 
## [27] "SMAD9"                   "GFPT2"                  
## [29] "PATJ"                    "TMTC1"                  
## [31] "DOCK11"                  "MYO1E"                  
## [33] "ARHGEF3"                 "FBN1"                   
## [35] "KIF5C"                   "CLIC4"                  
## [37] "CXXC5"                   "SLCO3A1"                
## [39] "SPATA13_ENSG00000182957" "NHS"                    
## [41] "TCEA3"                   "CTD-2054N24.2"          
## [43] "RP11-403A3.3"           
## [1] "found 38 genes."

## [1] 9
##  [1] "USH1C"       "CAP2"        "BEX2"        "MIPOL1"      "LMOD1"      
##  [6] "CES2"        "ADAP2"       "AQP1"        "KLHL13"      "MAP3K9"     
## [11] "CCDC124"     "PDZD4"       "PDK3"        "TRHDE"       "EBF4"       
## [16] "TSPAN11"     "NRP2"        "ASL"         "LRRC4B"      "TMCC2"      
## [21] "CCDC146"     "KIAA0513"    "TTLL7"       "EGF"         "CDR2"       
## [26] "CCDC40"      "MVB12A"      "SNTG1"       "TBX6"        "DEPTOR"     
## [31] "C1orf87"     "ZMAT4"       "REPS2"       "MOB3A"       "SYT12"      
## [36] "PPM1E"       "SWI5"        "ST8SIA3"     "YOD1"        "RASGEF1A"   
## [41] "NHSL2"       "AC004951.6"  "ATP6V0D1-DT"
## [1] "found 41 genes."

## [1] 10
##  [1] "SIPA1L2"  "APOC1"    "HESX1"    "SAMD4A"   "HDAC9"    "ATP9A"   
##  [7] "ATP2B4"   "CDON"     "PDE4A"    "PHACTR3"  "EEF2K"    "SYT17"   
## [13] "OLFM2"    "SIPA1L3"  "ABCC3"    "KLHL29"   "HIP1"     "EDA2R"   
## [19] "GFAP"     "HAVCR2"   "MAPK4"    "NFIC"     "ENSA"     "ITPKB"   
## [25] "BOC"      "TIAM2"    "CNKSR3"   "NCAM2"    "ARHGAP35" "FBXO27"  
## [31] "SLC20A2"  "DHRSX"    "IFFO2"    "NPAS2"    "SH3PXD2B" "PACS1"   
## [37] "SYNM"     "ZBTB7C"   "ZFP36L1"  "RILPL1"   "SRGAP1"   "MEF2B"   
## [43] "C19orf38"
## [1] "found 43 genes."

## [1] 11
##  [1] "MSMO1"    "YBX3"     "NTN1"     "SLC39A14" "RPL18A"   "RPL19"   
##  [7] "RPS15"    "HS3ST3B1" "RPL36"    "RPLP1"    "FAU"      "PBX3"    
## [13] "GLRX"     "RPS27"    "ZNF48"    "RPS18"    "CD99"     "VRK2"    
## [19] "CERS4"    "CTCF"     "COTL1"    "SLC7A5"   "KAT8"     "PLIN3"   
## [25] "KCNN1"    "NAMPT"    "UST"      "ECE1"     "RTN2"     "RTN3"    
## [31] "GLTP"     "RTN1"     "FSIP1"    "FGF17"    "ZER1"     "PKNOX2"  
## [37] "EVA1C"    "ZNF608"   "PTPN9"    "ANO6"     "CMTM4"   
## [1] "found 41 genes."

## [1] 12
##  [1] "XK"            "CALCRL"        "WSCD2"         "CCDC80"       
##  [5] "SLC8A3"        "PLCB4"         "IFI44L"        "HS3ST3A1"     
##  [9] "CHODL"         "ADAMTS9"       "GUCY1A1"       "WDR97"        
## [13] "CYP4F12"       "CYP4F3"        "CLDN4"         "RFX8"         
## [17] "STUM"          "INSYN2B"       "RP11-735G4.1"  "LINC01515"    
## [21] "LINC01768"     "DIRC3"         "LINC01725"     "DIRC3-AS1"    
## [25] "AC007563.5"    "LINC02814"     "LINC00407"     "AC092684.1"   
## [29] "SOCS2-AS1"     "RP11-364L4.3"  "RP11-124B13.1" "MAP1LC3B2"    
## [33] "RP11-354K4.2"  "LINC00836"     "LINC00842"     "RP11-364P22.4"
## [37] "RP11-492O8.3"  "RP11-96C13.1"  "CTD-2040G12.2" "RP11-259G3.1" 
## [41] "RP11-154D6.3"  "RP11-609L3.3"  "RP1-20N4.2"    "RP11-423B13.1"
## [45] "LINC02506"    
## [1] "found 19 genes."

## [1] 13
##  [1] "PRKAR2B"  "GAB2"     "CCDC85A"  "ELAVL2"   "PPM1H"    "MASP1"   
##  [7] "BTBD11"   "CADPS"    "ABTB2"    "ROBO2"    "PLEKHA5"  "SYT1"    
## [13] "RASAL2"   "RBFOX1"   "MAST3"    "DOK5"     "BNIP3L"   "SH3PXD2A"
## [19] "ZMIZ1"    "CPE"      "KIAA1217" "NAV1"     "ECE2"     "DIAPH2"  
## [25] "ZEB1"     "ANK3"     "MAGI1"    "AKAP6"    "TIAM1"    "SPTBN4"  
## [31] "SHANK1"   "PLEKHA7"  "RBFOX3"   "DLGAP1"   "DAB1"     "CNTNAP2" 
## [37] "RGS6"     "RALYL"    "KCNIP4"   "ELAVL3"   "ARID5A"   "RYR2"    
## [1] "found 41 genes."

## [1] 14
##  [1] "CDH10"         "PON3"          "DNAH7"         "DPH6"         
##  [5] "MAEL"          "HEG1"          "TMEM132C"      "SLC24A3"      
##  [9] "HDHD5-AS1"     "SULT1A2"       "DCHS2"         "AC074391.1"   
## [13] "SOX1-OT"       "POT1-AS1"      "PPP1R26-AS1"   "AC012593.1"   
## [17] "RP11-162D16.2" "SOX21-AS1"     "LNC-LBCS"      "XIST"         
## [21] "PPP1R9A-AS1"   "RP11-4B14.3"   "LINC00877"     "SUCLG2-AS1"   
## [25] "RP11-167H9.4"  "LINC02144"     "RP11-268P4.5"  "RP11-284M14.1"
## [29] "LINC00499"     "RP11-404I7.2"  "GS1-57L11.1"   "RP11-541P9.3" 
## [33] "RP11-134O21.1" "RMST"          "PRANCR"        "AC007193.6"   
## [37] "CTC-498M16.4"  "RP11-378A12.1" "RP4-681L3.3"   "RP11-175O15.1"
## [41] "RP11-346I3.7"  "RP11-563M4.2"  "CTD-2297M2.1"  "RP11-215I16.3"
## [1] "found 10 genes."

## [1] 15
##  [1] "DNAH9"        "MAOB"         "SEMA3A"       "SLC2A9"       "SH3D19"      
##  [6] "PHACTR2"      "DPYSL3"       "TACR1"        "LEPR"         "TFAP2E"      
## [11] "UBE3D"        "ENOX1"        "EEPD1"        "LYPD6B"       "PTH1R"       
## [16] "NDUFAF2"      "GALNT10"      "METTL2B"      "DPP10"        "GPR156"      
## [21] "CA8"          "EXT1"         "IMMP2L"       "SMYD3"        "APTR"        
## [26] "CTA-292E10.6" "SYNPO2L-AS1"  "HSD17B14"     "UBE2R2"       "ZBTB16"      
## [31] "ST8SIA1"      "SERPINI2"     "PLXDC2"       "HIVEP3"       "FCHO1"       
## [36] "GDPD5"        "ZNF704"       "WNK2"         "LDLRAD4"      "STX8"        
## [41] "KCND3"       
## [1] "found 38 genes."

## [1] 16
##  [1] "MGAT3"         "TACC2"         "FAM117B"       "FAXC"         
##  [5] "NXN"           "SLC43A2"       "LRRN2"         "RNLS"         
##  [9] "LMCD1-AS1"     "RP11-390F4.6"  "TRMT9B"        "CTD-2126E3.6" 
## [13] "GTF2IRD1"      "EYA2"          "RFX2"          "PCSK5"        
## [17] "MYO9B"         "COBL"          "RFX4"          "WLS"          
## [21] "ZC4H2"         "TICAM1"        "SEM1"          "ZBTB46"       
## [25] "RFTN1"         "RAP1GAP2"      "GMPR"          "ADAMTS10"     
## [29] "GABPB2"        "CLVS2"         "DENND2A"       "CLSTN2"       
## [33] "FAM107A"       "PIK3CD"        "C7orf61"       "HRH1"         
## [37] "PLCG2"         "LYRM4"         "KIF9-AS1"      "OLMALINC"     
## [41] "RP3-414A15.10" "FBXO17"       
## [1] "found 35 genes."

## [1] 17
##  [1] "ANKRD24"       "SEZ6L"         "MROH8"         "CPED1"        
##  [5] "GABRA4"        "DNAH6"         "BICC1"         "SLC14A1"      
##  [9] "FHAD1"         "ARHGAP18"      "SLC22A3"       "TEX9"         
## [13] "BEND6"         "PLEKHG4B"      "SPATA17"       "CA3"          
## [17] "ODAD2"         "RNF150"        "RNF212"        "C9orf153"     
## [21] "COL25A1"       "IL1RAPL2"      "ADD3-AS1"      "MT1H"         
## [25] "FBXO16"        "LINC01876"     "RP1-167A14.2"  "AC097721.2"   
## [29] "PATL2"         "RP11-120D5.1"  "LINC00886"     "RP11-11N9.4"  
## [33] "CTC-329D1.2"   "RP11-20I20.2"  "SPESP1"        "ADGRL1-AS1"   
## [37] "GEMIN7-AS1"    "PLS3-AS1"      "APP-DT"        "RP11-496B10.6"
## [41] "RP11-314E10.1" "DNAH5"         "TEKT1"         "NOL4L"        
## [45] "LINC00342"    
## [1] "found 28 genes."

## [1] 18
##  [1] "UPP2"           "MOGAT1"         "TMEM132B"       "EFCAB11"       
##  [5] "KIAA1328"       "MAP3K7CL"       "C11orf65"       "C12orf42"      
##  [9] "CATSPERE"       "LEKR1"          "FIRRE"          "LIPE-AS1"      
## [13] "AC007277.3"     "AC004540.5"     "LYPLAL1-DT"     "LINC01277"     
## [17] "RP11-498J9.2"   "MMADHC-DT"      "RFX3-AS1"       "RAP2C-AS1"     
## [21] "UFL1-AS1"       "RPL34-DT"       "NPIPB2"         "COX10-AS1"     
## [25] "LINC01376"      "RP11-550I24.2"  "RP11-461O7.1"   "RP11-669M16.1" 
## [29] "RP11-130F10.1"  "LINC01182"      "RP11-679C8.2"   "MAILR"         
## [33] "C8orf37-AS1"    "RP11-156K13.1"  "LINC02740"      "RP11-727A23.10"
## [37] "RP11-20E24.1"   "RP11-111A21.1"  "CTD-2349P21.11" "RP11-281A20.2" 
## [41] "RP11-69G16.2"   "RP4-660H19.2"   "RP11-168F16.1"  "RP5-921G16.1"  
## [1] "found 11 genes."

## [1] 19
##  [1] "RP1-230L10.1"   "LINC02715"      "TMEM38A"        "CATSPERG"      
##  [5] "CLIP2"          "NKD1"           "CCDC3"          "FAM151B"       
##  [9] "LMNTD1"         "LRGUK"          "ST3GAL2"        "CFAP251"       
## [13] "ORAI2"          "ZNF653"         "ARMC3"          "PDZRN4"        
## [17] "C2"             "ATOH8"          "NWD1"           "CFAP54"        
## [21] "TOGARAM2"       "ODAD4"          "NRSN2-AS1"      "LINC00884"     
## [25] "EPCAM-DT"       "HMGA1P4"        "RP11-305L7.3"   "MIR4300HG"     
## [29] "LINC01411"      "RP11-279O9.4"   "LINC01094"      "RP11-507B12.2" 
## [33] "RP11-507B12.1"  "ZNF594-DT"      "KLF2-DT"        "CTD-2189E23.1" 
## [37] "RP11-35G9.5"    "CASTOR2"        "RP11-154H23.4"  "RP11-514P8.10" 
## [41] "RP11-379B18.8"  "RP11-114N1.1"   "RP11-465L10.14" "RP11-301F14.1" 
## [45] "RP11-103P4.1"  
## [1] "found 20 genes."

## [1] 20
##  [1] "SLC26A8"        "SNAP25-AS1"     "LINC02763"      "COL5A3"        
##  [5] "WFDC1"          "XYLT1"          "LGR6"           "DOC2A"         
##  [9] "PID1"           "MRAS"           "ESYT3"          "RANBP3L"       
## [13] "CHST11"         "CSDC2"          "MRGPRF"         "HPSE2"         
## [17] "CALCB"          "FZD8"           "CTD-2527I21.15" "NME9"          
## [21] "ZNF804B"        "FLRT2"          "NOTUM"          "FZD9"          
## [25] "AJAP1"          "ZNF98"          "TMEM184B"       "HRAT92"        
## [29] "AC064875.2"     "HPN-AS1"        "AC003991.3"     "SPRY4-AS1"     
## [33] "AC002127.4"     "PDYN-AS1"       "AC016745.3"     "ETV5"          
## [37] "LINC02208"      "LINC01414"      "LINC01619"      "RP11-328J6.1"  
## [41] "CEACAM16-AS1"   "PKD1L3"         "RP11-237N2.1"   "RP11-183J19.1" 
## [1] "found 26 genes."

## [1] 21
##  [1] "COL4A2"        "RP4-613B23.1"  "BAIAP3"        "APBA2"        
##  [5] "TLE2"          "ITPKC"         "P2RX7"         "CDKL1"        
##  [9] "TUSC3"         "FGL1"          "CHRNE"         "ARSB"         
## [13] "PADI2"         "COL21A1"       "PRR12"         "PTPRE"        
## [17] "PLCE1"         "RHBDL3"        "ADCY8"         "SLC5A11"      
## [21] "TMCO4"         "SHISA5"        "EDIL3"         "ELAPOR2"      
## [25] "TMC1"          "GPR176"        "NPNT"          "LINGO1"       
## [29] "SLC26A5"       "FRMD3"         "GPR137C"       "SPACA6"       
## [33] "TSHZ2"         "UTY"           "DMWD"          "COL27A1"      
## [37] "LINC00685"     "RP5-864K19.4"  "RP5-1198O20.4" "L3MBTL2-AS1"  
## [41] "KCNK15-AS1"    "RP3-466I7.2"  
## [1] "found 35 genes."

## [1] 22
##  [1] "PRKCQ"    "EPHA6"    "SCG3"     "EPM2A"    "GBE1"     "EPHA4"   
##  [7] "PPP1R3C"  "CCDC59"   "C10orf90" "TSPAN5"   "SNTB1"    "STOX2"   
## [13] "ROR1"     "KLHL32"   "SHISA6"   "VKORC1L1" "TENM3"    "MRPL33"  
## [19] "ITGA3"    "COL23A1"  "MCF2L2"   "SYNE2"    "CAMK2B"   "TBC1D1"  
## [25] "RARB"     "DNM1"     "PPARGC1A" "DMGDH"    "VAV3"     "CCNH"    
## [31] "TNS3"     "SDK1"     "DGKZ"     "ABCB9"    "THRB"     "RFTN2"   
## [37] "ALK"      "ABAT"     "EFNA5"    "PARVA"    "DNM3"    
## [1] "found 41 genes."

## [1] 23
##  [1] "RP11-104E19.1"           "USH2A"                  
##  [3] "LAMB4"                   "SLC26A3"                
##  [5] "STEAP1B"                 "BEST3"                  
##  [7] "SCN2A"                   "CBLN2"                  
##  [9] "SLC4A10"                 "CDH18"                  
## [11] "ZNF385D"                 "SLC24A2"                
## [13] "GREM1"                   "HTR1E"                  
## [15] "SEMA3E"                  "KCNH7"                  
## [17] "CACNA1E"                 "MMP17"                  
## [19] "AC023469.1"              "RP11-191L9.4"           
## [21] "RP1-35C21.2"             "RP11-147G16.1"          
## [23] "RP11-154D17.1"           "RP5-827C21.2"           
## [25] "SHISA9"                  "AC002066.1"             
## [27] "CTC-340A15.2"            "RP11-384F7.1"           
## [29] "RP11-17A1.3"             "RP11-446J8.1"           
## [31] "RP11-26J3.1"             "LINC02742"              
## [33] "LINC01609"               "RP11-20D14.3"           
## [35] "RP11-499F3.2"            "LINC00558"              
## [37] "MTRNR2L12"               "RMRP_ENSG00000269900"   
## [39] "SCARNA2_ENSG00000270066" "CH507-513H4.1"          
## [41] "CH507-528H12.1"          "RP4-799O8.1"            
## [43] "AC003099.2"              "RP11-398J12.1"          
## [45] "RP11-4D11.1"            
## [1] "found 19 genes."

## [1] 24
##  [1] "NID1"           "F3"             "MT1G"           "MTERF1"        
##  [5] "PUDP"           "AGBL3"          "MN1"            "MT1E"          
##  [9] "SGCD"           "MACROD2"        "CYP7B1"         "DLEU1"         
## [13] "CC2D2B"         "COL28A1"        "AC072062.3"     "Z83001.1"      
## [17] "HDAC2-AS2"      "RP11-154D6.1"   "OBI1-AS1"       "RNF217-AS1"    
## [21] "PTPRG-AS1"      "SOX2-OT"        "RP11-373N22.3"  "LINC00504"     
## [25] "LINC01950"      "RP11-582J16.4"  "LIX1-AS1"       "RP11-673E1.1"  
## [29] "LINC02328"      "AC004158.3"     "LINC01572"      "RP11-436D23.1" 
## [33] "LINC02664"      "RP11-470M1.2"   "RP11-437L7.2"   "RP11-692P14.1" 
## [37] "RP11-1289C17.1" "RP11-520F22.1"  "UNC5B"          "TGIF2"         
## [41] "TENM2"          "FAXDC2"         "KBTBD12"        "LINC01252"     
## [1] "found 18 genes."

## [1] 25
##  [1] "NRXN3"       "ZFR2"        "RGS4"        "UNC13A"      "CALY"       
##  [6] "TESPA1"      "PLK2"        "MLIP"        "LRRIQ3"      "ANKRD33B"   
## [11] "GRIK2"       "NEGR1"       "GALNTL6"     "RGS7"        "KCTD16"     
## [16] "CCSER1"      "STAC3"       "PCLO"        "SLIT1"       "ERC2"       
## [21] "DLGAP2"      "PWRN1"       "RIMS1"       "ATRNL1"      "KHDRBS2"    
## [26] "PDE1A"       "RIMS3"       "ZNF385B"     "CNTN5"       "GRM5"       
## [31] "NLGN1"       "FRMPD4"      "ARPP21"      "NABP1"       "RIMS2"      
## [36] "SAMD12"      "OPCML"       "SYN3"        "KCNQ5"       "PTPRT"      
## [41] "RP1-30E17.2" "PCAT1"      
## [1] "found 39 genes."

## [1] 26
##  [1] "STK32A"        "BNC2"          "RP11-116N8.1"  "ST6GALNAC2"   
##  [5] "FAP"           "SLCO1A2"       "JHY"           "SOHLH2"       
##  [9] "LRAT"          "TTC9"          "SCN1A"         "HNMT"         
## [13] "CCDC175"       "PARP8"         "ANGPT1"        "GAL3ST2"      
## [17] "DRC1"          "NFASC"         "CFAP47"        "SLITRK5"      
## [21] "COL24A1"       "PRIMA1"        "PLCXD3"        "OVCH1"        
## [25] "LAMA2"         "AC003090.1"    "AC092155.4"    "RP11-69I8.3"  
## [29] "RP1-111D6.3"   "RP11-469A15.2" "RP11-146I2.1"  "RP11-90C4.1"  
## [33] "AL163953.3"    "CTD-2643I7.5"  "RP11-190P13.2" "LINC01088"    
## [37] "CTB-35F21.1"   "LINC00609"     "LINC02251"     "RP11-259K15.2"
## [41] "RP11-627D16.1" "RP11-210M15.2" "RP11-876N24.2" "RP1-79C4.4"   
## [45] "RP11-6L16.1"  
## [1] "found 24 genes."

## [1] 27
##  [1] "CD38"          "SP140"         "SPATA6L"       "PAPPA2"       
##  [5] "RNF175"        "DNAAF1"        "PKD1L1"        "STPG2"        
##  [9] "SCN11A"        "ZBTB44-DT"     "CASC2"         "RFLNA"        
## [13] "RHCE"          "SCOC-AS1"      "COL5A2"        "MALRD1"       
## [17] "CHL1-AS2"      "AP001628.6"    "TARID"         "AC008269.2"   
## [21] "ZRANB2-AS2"    "LINC00271"     "LINC01524"     "RP11-195C7.1" 
## [25] "LINC01829"     "LEFTY1"        "DRAIC"         "CTB-161M19.4" 
## [29] "RP11-1252I4.2" "RP4-785G19.5"  "CTC-347C20.1"  "LINC02320"    
## [33] "RP11-739G5.1"  "RP11-525K10.3" "DISC1FP1"      "RP11-396B14.2"
## [37] "RP11-397A16.1" "AC005786.7"    "RP11-157E16.1" "LINC00506"    
## [41] "RP11-964E11.3" "RP11-274G22.1" "RP11-382N13.7" "RP11-444C24.1"
## [45] "RP5-892C22.1" 
## [1] "found 14 genes."

## [1] 28
##  [1] "CTD-2313D3.2"          "ADGRL1"                "SEC14L5"              
##  [4] "DGKB"                  "UNC13C"                "ST18"                 
##  [7] "PLCL2"                 "CFAP161"               "SYTL3"                
## [10] "ADCY1"                 "TVP23A"                "GSG1L"                
## [13] "RCAN2"                 "PPP1R42"               "SLC8A1"               
## [16] "OSBP2"                 "FAM174B"               "RTN4RL1"              
## [19] "CCDC30"                "PDE2A"                 "SHTN1"                
## [22] "PAX8-AS1"              "LINC00632"             "TNFRSF25"             
## [25] "AP001347.6"            "XXbac-BPG55C20.7"      "TSBP1-AS1"            
## [28] "RP11-563D10.1"         "LINC01320"             "WARS2-AS1"            
## [31] "CYP1B1-AS1"            "AC067956.1"            "LINC02223"            
## [34] "RP11-79E3.2"           "RP11-624C23.1"         "LINC02356"            
## [37] "RP11-148E17.1"         "RPPH1_ENSG00000259001" "RP11-838N2.5"         
## [40] "DGCR5_ENSG00000273032" "SPANXA2-OT1"           "RP11-596C23.6"        
## [43] "IQCJ-SCHIP1"           "RP11-114N19.3"         "RP1-166D18.1"         
## [1] "found 22 genes."

## [1] 29
##  [1] "MTCL1"         "LINC02884"     "ARHGAP31"      "DGKG"         
##  [5] "KIF3C"         "MYOM1"         "CAB39L"        "AGFG2"        
##  [9] "LGI1"          "RIPOR2"        "TFDP2"         "PDZRN3"       
## [13] "TOX2"          "HIF3A"         "SYNE1"         "IQCA1"        
## [17] "RIN2"          "SHROOM3"       "FAM171A1"      "FAM13C"       
## [21] "CNNM2"         "GRIK4"         "AHCYL2"        "DHRS3"        
## [25] "GNG4"          "ZFPM2"         "FAM222B"       "TCAP"         
## [29] "IQCK"          "PHYHD1"        "NCKAP5"        "SLC25A20"     
## [33] "APOLD1"        "ARL15"         "TPCN1"         "TRPV1"        
## [37] "ZNF785"        "TOX"           "EFCAB2"        "HAUS7"        
## [41] "LINC01135"     "AGBL1"         "RP11-799O21.2"
## [1] "found 40 genes."

## [1] 30
##  [1] "ARHGAP44"      "HHAT"          "SDK2"          "STS"          
##  [5] "WNT5B"         "TENT5A"        "PLAGL1"        "GTDC1"        
##  [9] "UNC79"         "PKIB"          "ARSG"          "SUMF1"        
## [13] "TMEM108"       "ACSL1"         "SLC9B1"        "ALDH1A1"      
## [17] "JAM3"          "ANO5"          "PNMA3"         "KIAA0825"     
## [21] "MAML3"         "BRINP2"        "MAMDC2-AS1"    "RP11-306O13.1"
## [25] "LINC00571"     "AC026188.1"    "LINC01937"     "PKN2-AS1"     
## [29] "H2AZ1-DT"      "LINC02355"     "RP11-804N13.1" "MPPED2-AS1"   
## [33] "RP11-624D11.2" "RP11-511B23.2" "RP11-72M17.1"  "RP11-798K3.2" 
## [37] "IDH2-DT"       "PSMD7-DT"      "LINC00907"     "TSIX"         
## [41] "CTC-490G23.6"  "RP11-221G19.1" "CPM"          
## [1] "found 23 genes."

## [1] 31
##  [1] "MRC2"          "FAM107B"       "REEP1"         "KCNN2"        
##  [5] "SGK2"          "RIPK2"         "NT5DC3"        "B3GAT2"       
##  [9] "WIPF1"         "ADCY7"         "IFI6"          "TRIM5"        
## [13] "EPHB2"         "AVIL"          "ARRDC4"        "LPAR4"        
## [17] "MON1A"         "FABP5"         "PRTG"          "SCG5"         
## [21] "C1QTNF4"       "GINS3"         "PIWIL2"        "L3MBTL3"      
## [25] "SAMD13"        "HLA-E"         "LGALSL-DT"     "LRRC24"       
## [29] "RP11-373E16.6" "ARHGAP6"       "ADAP1"         "CLSTN3"       
## [33] "TMEM200A"      "NT5DC2"        "SPSB1"         "PAWR"         
## [37] "FAM110C"       "OSTN"          "AC013463.2"    "CRYBB2"       
## [41] "RP11-542F9.2"  "RP11-93B21.2" 
## [1] "found 37 genes."

## [1] 32
##  [1] "MBNL3"         "MT3"           "SRPX"          "IL7"          
##  [5] "PSG8"          "APOE"          "TMEM160"       "EMP1"         
##  [9] "PDE5A"         "ABCA12"        "HMGA2"         "GFRA1"        
## [13] "DLC1"          "LRRC3B"        "PLD5"          "MT1X"         
## [17] "PTMA"          "EYS"           "KCNMB2"        "HES5"         
## [21] "RANBP17"       "ANKUB1"        "AC009501.4"    "GNG12-AS1"    
## [25] "RP5-1101C3.1"  "LUCAT1"        "CTD-2015H6.3"  "VCAN-AS1"     
## [29] "RP11-517I3.1"  "ZFPM2-AS1"     "RP11-649G15.2" "CTD-2537O9.1" 
## [33] "PTCSC3"        "RHOBTB1"       "ARID3A"        "FREM2"        
## [37] "PTMS"          "OXR1"          "CKB"           "CRADD"        
## [41] "PDE3A"         "ZMAT3"         "DUSP8"        
## [1] "found 32 genes."

## [1] 33
##  [1] "LINC01931"     "HHIP"          "CLMP"          "GLIPR1L1"     
##  [5] "P2RY14"        "SGCZ"          "FSIP2"         "RNF212B"      
##  [9] "HEPN1"         "AC002463.3"    "RP11-131L23.1" "RP4-660H19.1" 
## [13] "RP11-547I7.1"  "ST7-AS2"       "PCDH9-AS2"     "GPC5-AS2"     
## [17] "GRM3-AS1"      "PCDH9-AS4"     "RP11-109I13.2" "LINC02250"    
## [21] "AC008067.2"    "RP11-475C16.2" "RP13-143G15.4" "LINC02877"    
## [25] "RP11-657O9.1"  "ZBTB20-AS5"    "LINC00960"     "GK-AS1"       
## [29] "RP11-115N4.1"  "RORA-AS1"      "LRP4-AS1"      "MAPK10-AS1"   
## [33] "RP11-116O11.1" "STPG2-AS1"     "RP11-351A11.1" "RP11-463D19.1"
## [37] "AP000462.2"    "RP11-370I10.2" "LINC01579"     "DIO2-AS1"     
## [41] "RP11-39M21.1"  "CTD-2282P23.2" "RP11-576O3.1"  "RP11-394G3.3" 
## [45] "RP11-66G15.1" 
## [1] "found 8 genes."

## [1] 34
##  [1] "IDI1"         "BLVRB"        "PLS3"         "SLC1A2"       "GMDS"        
##  [6] "MT2A"         "CABLES1"      "PRR5L"        "C4orf19"      "ABHD3"       
## [11] "CMSS1"        "MALAT1"       "SESN1"        "PALM"         "DAAM1"       
## [16] "CDH20"        "ARHGEF18"     "CPEB3"        "TANC1"        "C1orf21"     
## [21] "ZFP36"        "ZSWIM6"       "ADGRB3"       "ARHGAP29"     "JAZF1"       
## [26] "GNA14"        "NRG2"         "PTCHD1"       "CACNB2"       "NAV2"        
## [31] "PCDH7"        "CADM2"        "GNG7"         "LDLRAD3"      "FIGN"        
## [36] "LHFPL6"       "MAML2"        "CPEB1"        "LINC00511"    "DLEU2"       
## [41] "PTCHD1-AS"    "TMEM161B-AS1"
## [1] "found 37 genes."

## [1] 35
##  [1] "RRAGD"         "AHRR"          "BCAS1"         "ARHGAP28"     
##  [5] "SLC16A6"       "TRIM22"        "FHDC1"         "DUSP15"       
##  [9] "RETREG1"       "GFRA2"         "DELEC1"        "SNX31"        
## [13] "CIITA"         "CYP4X1"        "IER5L"         "NPSR1-AS1"    
## [17] "LINC01117"     "LINC01630"     "RP1-223B1.1"   "LINC01503"    
## [21] "AC009264.1"    "MSC-AS1"       "PRKAR2B-AS1"   "LINC02217"    
## [25] "LINC01618"     "LINC00958"     "RP11-745L13.2" "CENATAC-DT"   
## [29] "LINC02327"     "LINC00637"     "LINC02254"     "MAPT-AS1"     
## [33] "RP1-41C23.1"   "RP11-355F16.1" "RP11-323P17.2" "PRAG1"        
## [37] "RP5-965G21.3"  "LINC01374"     "RP11-239A17.1" "CTC-428H11.2" 
## [41] "RP11-313M3.2"  "AC006296.4"    "MCUB"          "PLPP4"        
## [45] "RP11-403A3.2" 
## [1] "found 17 genes."

## [1] 36
##  [1] "CD200R1"       "GRK3"          "TFCP2L1"       "ACVR1C"       
##  [5] "LRMDA"         "KCNE4"         "TDRD9"         "SHROOM4"      
##  [9] "FAAH2"         "METTL7B"       "SLC25A18"      "PLK5"         
## [13] "TRDN"          "NKAIN2"        "C3orf35"       "LINC00862"    
## [17] "PLIN5"         "RP11-174G6.1"  "AP000318.2"    "LINC00598"    
## [21] "ARL17B"        "AC104088.1"    "LINC01137"     "KCNMB2-AS1"   
## [25] "ARHGEF26-AS1"  "RTL9"          "ALDH1L1-AS2"   "STX18-AS1"    
## [29] "DPH6-DT"       "LINC02315"     "RP11-346L1.2"  "RP11-298I3.1" 
## [33] "RP11-150C16.1" "CASC17"        "RP1-158P9.2"   "TAPT1-AS1"    
## [37] "RP11-60A24.3"  "AC079610.1"    "RP11-711K1.8"  "LINC02246"    
## [41] "RP11-26L21.1"  "RP11-166M16.1" "RP11-404C6.6"  "RP11-125C10.1"
## [1] "found 17 genes."

## [1] 37
##  [1] "MAMLD1"        "SNCAIP"        "PNPLA3"        "GALNT16"      
##  [5] "LAMA4"         "SLC24A4"       "SYCP2L"        "ABI3BP"       
##  [9] "HNF4G"         "SUGCT"         "SLC4A5"        "LINC02649"    
## [13] "RP11-344B5.2"  "SNHG31"        "AF131217.1"    "LINC02652"    
## [17] "LINC02234"     "NEUROG2-AS1"   "MGAM"          "FRMD6-AS2"    
## [21] "RP11-571L19.7" "RP11-574F11.4" "NIPAL3"        "CNTN1"        
## [25] "ATP1A2"        "RNF19A"        "RNF24"         "PPP1R13L"     
## [29] "B4GALT2"       "NCAN"          "SLC39A11"      "ARHGEF4"      
## [33] "BCAS3"         "KCNN3"         "SEMA3D"        "PDPN"         
## [37] "ABCA1"         "FAT3"          "SLC35E3"       "RGMA"         
## [41] "CNTN2"         "TMEM229B"      "EML6"         
## [1] "found 33 genes."

## [1] 38
##  [1] "ASB4"     "TENM1"    "MYO16"    "TRPM3"    "ID2"      "BEX1"    
##  [7] "CD72"     "CXCL14"   "IGFBP7"   "ALCAM"    "RIMBP2"   "CTNNA2"  
## [13] "ISYNA1"   "GLIS3"    "CLNK"     "LIN7A"    "TPD52L1"  "CCND3"   
## [19] "CTSD"     "STAG1"    "FOXO3"    "TEX11"    "MACF1"    "PALLD"   
## [25] "SOX5"     "SSH2"     "PAM"      "ARHGAP26" "FOXO1"    "DST"     
## [31] "MGAT5"    "ART3"     "C2CD2"    "ABR"      "PFKFB3"   "FRMD5"   
## [37] "MYO1D"    "LSMEM2"   "CADM1"    "PCP4"     "IRS2"     "NEAT1"   
## [1] "found 41 genes."

## [1] 39
##  [1] "CA1"            "WDR64"          "SHOC1"          "FILIP1L"       
##  [5] "SEPTIN1"        "TSBP1"          "TMLHE-AS1"      "AC105461.1"    
##  [9] "AC017101.10"    "ASTN2-AS1"      "RP11-141A19.1"  "RP11-417B4.2"  
## [13] "GNA14-AS1"      "RP11-46O21.2"   "LINC00513"      "AC037445.1"    
## [17] "STARD13-AS"     "GS1-433O24.1"   "LINC01877"      "RP11-768G7.3"  
## [21] "RP11-274H2.2"   "ANK2-AS1"       "RP11-223C24.1"  "RP11-348J24.1" 
## [25] "RP11-120A1.1"   "RP11-39E3.3"    "CTD-3239E11.2"  "BBOX1-AS1"     
## [29] "RP11-1H15.2"    "RP11-513G19.1"  "A2ML1-AS1"      "RP11-315E17.1" 
## [33] "RP11-887P2.5"   "RP11-184D12.1"  "CRIM1-DT"       "RP11-58G13.1"  
## [37] "RP11-138H11.1"  "RP11-80I3.1"    "CH17-140K24.2"  "RP11-793H13.14"
## [41] "CTD-2172F7.1"   "RP11-555K12.4"  "DNAH11"         "ZNF208"        
## [45] "LINC01208"     
## [1] "found 8 genes."

## [1] 40
##  [1] "ANOS1"         "PCSK1N"        "SRPX2"         "POLR2I"       
##  [5] "PDE8B"         "GDAP1L1"       "H3-3B"         "ITGA9"        
##  [9] "LRTM1"         "CHST9"         "MEGF11"        "BTG2"         
## [13] "MFSD4B"        "HES4"          "CARNMT1-AS1"   "RP11-106M7.1" 
## [17] "DPP10-AS3"     "IPO9-AS1"      "RP11-666F17.1" "DPP10-AS1"    
## [21] "RP11-446H18.5" "CDKN2B-AS1"    "BAALC-AS1"     "SEMA6A-AS1"   
## [25] "C1QTNF7-AS1"   "RP11-711G10.1" "RP11-157I4.4"  "RP11-452H21.1"
## [29] "AP000487.6"    "RP11-144F15.1" "RP11-363J20.2" "HIF1A-AS3"    
## [33] "PRKCA-AS1"     "CTC-513N18.6"  "ARRDC3-AS1"    "SLC7A14-AS1"  
## [37] "RP11-589M4.5"  "BCL6-AS1"      "RP11-125D12.3" "RP11-725F23.1"
## [41] "RP11-592G13.2" "RP11-875G18.1" "NUP210L"      
## [1] "found 15 genes."

Session information

gc()

##           used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells 4155659 222.0    7959177 425.1         NA  7959177 425.1
## Vcells 8941387  68.3   29538339 225.4      65536 29317758 223.7

sessionInfo()

## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] stringr_1.5.0     limma_3.54.2      tidyr_1.3.0       ggpubr_0.6.0     
## [5] ggplot2_3.4.2     data.table_1.14.8
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.10            png_0.1-8              Biostrings_2.66.0     
##  [4] digest_0.6.31          utf8_1.2.3             R6_2.5.1              
##  [7] GenomeInfoDb_1.34.9    backports_1.4.1        stats4_4.2.3          
## [10] RSQLite_2.3.1          evaluate_0.20          httr_1.4.6            
## [13] pillar_1.9.0           zlibbioc_1.44.0        rlang_1.1.0           
## [16] rstudioapi_0.14        car_3.1-2              jquerylib_0.1.4       
## [19] blob_1.2.4             R.oo_1.25.0            R.utils_2.12.2        
## [22] S4Vectors_0.36.2       rmarkdown_2.21         labeling_0.4.2        
## [25] RCurl_1.98-1.12        bit_4.0.5              munsell_0.5.0         
## [28] broom_1.0.4            compiler_4.2.3         xfun_0.39             
## [31] pkgconfig_2.0.3        BiocGenerics_0.44.0    htmltools_0.5.5       
## [34] tidyselect_1.2.0       KEGGREST_1.38.0        GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1           IRanges_2.32.0         fansi_1.0.4           
## [40] crayon_1.5.2           dplyr_1.1.2            withr_2.5.0           
## [43] R.methodsS3_1.8.2      bitops_1.0-7           grid_4.2.3            
## [46] jsonlite_1.8.4         gtable_0.3.3           lifecycle_1.0.3       
## [49] DBI_1.1.3              magrittr_2.0.3         scales_1.2.1          
## [52] cli_3.6.1              stringi_1.7.12         cachem_1.0.7          
## [55] carData_3.0-5          farver_2.1.1           XVector_0.38.0        
## [58] ggsignif_0.6.4         bslib_0.4.2            generics_0.1.3        
## [61] vctrs_0.6.2            RColorBrewer_1.1-3     org.Hs.eg.db_3.16.0   
## [64] tools_4.2.3            bit64_4.0.5            Biobase_2.58.0        
## [67] glue_1.6.2             purrr_1.0.1            abind_1.4-5           
## [70] fastmap_1.1.1          yaml_2.3.7             AnnotationDbi_1.60.2  
## [73] colorspace_2.1-0       rstatix_0.7.2          memoise_2.0.1         
## [76] knitr_1.44             sass_0.4.5